Darwin wins: Harbaugh basing QB decision on skills, not sentiment

He’s a quarterback that’s won plenty of games for Jim Harbaugh and, in return, the coach has backed him with such over-the-top oratory fervor that many have rolled their eyes.

Given their history, could Harbaugh really turn away from a guy many have viewed as “his guy”?

The answer? Uh, yeah. Weren’t you paying attention when he did it this summer?

The quarterback in question here, you see, is not Alex Smith, but Josh Johnson.

Johnson started for two seasons under Harbaugh at then non-scholarship, Division I-AA University of San Diego, leading the Toreros to a 22-2 record and mid-major national titles in 2005 and ’06.

During Johnson’s junior season, Harbaugh declared he was “the best quarterback in college football, period,” which may have surprised those who preferred Boston College’s Matt Ryan or Delaware’s Joe Flacco. Last year, before the 49ers played Tampa Bay, where Johnson was the backup, Harbaugh said he viewed Johnson “like a beloved son.”

It’s not known if Johnson ever lugged Harbaugh’s golf bag around Torrey Pines, but when he signed with the 49ers in the offseason it was assumed their shared history would give Johnson an unspoken edge. He would certainly win a roster spot (sorry, Scott Tolzien), challenge Colin Kaepernick for the backup spot and, perhaps, threaten Alex Smith in future seasons.

Instead, The Beloved Son was released with 20 other players on Aug. 31 during final roster cuts. Harbaugh said Johnson lost a “dead heat” with Tolzien for the No. 3 quarterback spot. The tie didn’t go to his guy, but to the better quarterback, in Harbaugh’s estimation.

“Darwin wins,” Harbaugh said on Sept. 1 in discussing the overall winnowing of the roster. “It’s the survival of the fittest. The strong survive.”

Three months later, Harbaugh has apparently determined Kaepernick, with his bazooka arm, uncommon escapability and beyond-his-years poise, has matured into fittest of his quarterbacks.

Could Harbaugh still pull a jaw-dropper Wednesday and announce he’s sticking with Smith? Anything’s possible, of course, but if he does so it won’t be for sentimental reasons. With Harbaugh, you can be certain the decision will be based solely on which quarterback he believes gives the 49ers the best chance to win. He’s loyal to the team, not Smith.

Given Harbaugh’s eye for quarterback talent, that’s good news for fans, if potential bad news for the guy with the weaker arm and slower 40.